sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2c1dc33d99a89e024f6ecc031bf2585d74e60a8108016e8f6b63011e5b049f8f | C++ | 5,247 | 140 | #include <algorithm>
#include <vector>
#include "caffe/layers/sigmoid_cross_entropy_loss_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void SigmoidCrossEntropyLossLayer<Dtype>::LayerSetUp(
const vector<Blob<Dtype>*>& bottom, const vector<Blob<Dtype>*>& top) {
L... |
121ac20a374c095d1bdf09eefd23487a3aa378f6f7342bc8883c83773cc6f24f | C++ | 5,265 | 178 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
*
* blockedSummation.cpp
*
* Code generation for function 'blockedSummation'
*
*/
/* Include files */
#include... |
245917f5e05b3ce1cd766d81dd34b548c3d400f14e8df6172d0c2f8a5f1cef1b | C++ | 5,297 | 143 | /**
* Copyright 2022-2024, XGBoost contributors.
*/
#include <gtest/gtest.h>
#include <xgboost/base.h> // for bst_node_t
#include <xgboost/context.h> // for Context
#include <algorithm> // for transform
#include <iterator> ... |
c4f68a9a75080989d8911a751386ff342f8f82f4a6ac4dcf330a3f0ddbb0e0ad | C++ | 5,302 | 159 | // Copyright 2005, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
dc08474abf56922cdcf7611d8ee7537cc9e1c95d49c7323e6be5ae99654b509a | C++ | 5,305 | 156 | // Copyright 2007, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
15e80a6c4ec773a4069f501c556483965bdf3dcf0e6852d567ef3a4c656f7b45 | C++ | 5,323 | 201 | /* coding=utf-8
* Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*... |
bac49f38c6f7c05e7ee02f86c72b5e08fdece3dff02b042de8896ad309c2de6d | C++ | 5,340 | 136 | #include "Masker.h"
#include <algorithm> // for std::toupper
Masker::Masker(BaseMatrix &s) : subMat(s), probMatrix(s)
{
maxSeqLen = 1;
charSequence = (unsigned char *)malloc(maxSeqLen * sizeof(char));
maskLetterNum = subMat.aa2num[(int)'X'];
}
Masker::~Masker() {
free(charSequence);
}
int Masker::mas... |
095c34e94eac9e911d274e21c228112e717381634093a648711666b051dd6c2c | C++ | 5,342 | 167 | #ifdef USE_HDF5
#include <string>
#include <vector>
#include "hdf5.h"
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/layers/hdf5_data_layer.hpp"
#include "caffe/proto/caffe.pb.h"
#include "caffe/test/test_caffe_main.hpp"
namespace caffe {
template <typename TypePara... |
a023b3cbefa3f4aab1f8ed43270c9d1ce8f0070b93e2051c9d9973b81bc45280 | C++ | 5,425 | 135 | #include "stdafx.h"
#include "ProbabilityDistance.h"
#include "Compat.h"
#ifdef TRACE_PROBABILITY_DISTANCE
#define TRACE printf
#else
#define TRACE(...) {}
#endif
namespace {
inline double max3(double d1, double d2, double d3) {
if (d1 > d2) {
return (d1 > d3) ? d1 : d3;
} else {
... |
352acab1e5cfa0e2eac5171244fe5b9fb51e4ca800676861cc69ae7ed5da03df | C++ | 5,428 | 189 | /*
* Based on https://github.com/TuftsBCB/io
* Ported from GO to C++
* License:
* Copyright (c) <2013> <Andrew Gallant>
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restr... |
3ac4eca8cb28d3baa1bc476fe2f508719139fcfba22453dceb1d5201b6bb70d3 | C++ | 5,437 | 127 | // Copyright 2007, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
510aef6e493e0f78dc844fd98cae6702ef2444a7115e69e208d04546ec3b1ff7 | C++ | 5,473 | 174 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
e8e525b80d4d1a9cdeedcf25bce84c3c0ca0a076abb8c7173d82d4e2329f1fc0 | C++ | 5,475 | 202 | /*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your opt... |
03eb6f03f9011b12ea6e3182c85b07224ccdf6eb5b8223f0bacdd675f2dc821a | C++ | 5,485 | 328 | # include <stdio.h>
# include <stdlib.h>
# include <math.h>
static int
svbksb (double **u, double *w, double **v, int m, int n, double *b, double *x)
{
int i, j, k;
double s, tmp[n+1];
for (j=1; j<=n; j++) {
s = 0.;
if (w[j] != 0.) {
for (i=1; i<=m; i++)
s += u[i][j]*b[i];
s /= w[j];
}
tmp[j] =... |
9bf9d1872482b7807ebb209036a0828b01f049ac27d58e73ba1ffbb94ec5b5b2 | C++ | 5,496 | 201 | /*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your opt... |
d6cea8b69cd0d4c91f922ddf4e8a9a9864f31b456df3dd458825c77ab5c5c6e1 | C++ | 5,506 | 123 | // dear imgui: standalone example application for Marmalade
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
// Copyright (C) 2015 by Giovanni Zito
// This file is part of Dear ImGui
#include "imgui.h"
#include "imgui_impl_marmalade.h"
#include <stdio.h>
#include <s... |
fdbf7672d9ffa8bce91f329f970f7736ee2202d9325ff4411bf845ae5423b1f3 | C++ | 5,511 | 175 | /******************************************************************
* *
* Copyright by Joachim Saul <saul@gfz-potsdam.de> *
* *
***********************************************... |
ad1e7558b99fd151fc39f8f6c63d2a1daf9764662f2f3ec6413c9ca437264949 | C++ | 5,524 | 149 | #include "Windows.h"
#include "mex.h"
#include <map>
#include <string>
#include <stdexcept> // std::out_of_range
using namespace std;
static DWORD nInitializedHandles = 0;
static map<string, HANDLE> eventsMap;
static HANDLE* pEventHandles;
void Delete(void)
{
for (auto it = begin(eventsMap); it!=end(eventsM... |
96b0a11592c49775cedcf64679511c3745c914d6d243cdcf5ba4e0190be3f054 | C++ | 5,530 | 152 | #include <algorithm>
#include <functional>
#include <map>
#include <set>
#include <vector>
#include "caffe/layer.hpp"
#include "caffe/layers/crop_layer.hpp"
#include "caffe/net.hpp"
namespace caffe {
template <typename Dtype>
void CropLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
const vector<Bl... |
9d274b85c739a85d218d3d3c96628643d091b1c6de1d77399c192d326858bbb6 | C++ | 5,547 | 150 | #include <vector>
#include "caffe/filler.hpp"
#include "caffe/layers/inner_product_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void InnerProductLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
const vector<Blob<Dtype>*>& top) {
const int num_out... |
97ab6a1cd3c12ec3438ae725cf3521f7cafe075a01223d59d4312a6b364ca2e8 | C++ | 5,555 | 148 | #include <cmath>
#include <vector>
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layers/sigmoid_cross_entropy_loss_layer.hpp"
#include "caffe/test/test_caffe_main.hpp"
#include "caffe/test/test_gradient_check_util.hpp"
namespace caffe {
t... |
f74a4371adc6385785df35c5177807c60f80112c1500dc8f4233dc7e22925350 | C++ | 5,556 | 220 | // Copyright 2008, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
8fd91b6ae4682311e5bc515fe2eca745286416bae1150101d17bdf09d20c4ebf | C++ | 5,566 | 153 | #include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "itoa.h"
#include <list>
#ifdef OPENMP
#include <omp.h>
#endif
int mergeclusters(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, comman... |
c49dc4ee52345808f9e25e49fa26964d2f72def0b7025a7164b4fa3a8a1496e4 | C++ | 5,601 | 64 | #include "Command.h"
#include "Parameters.h"
std::vector<std::vector<Command>*> commands;
void registerCommands(std::vector<Command>* cmd) {
commands.emplace_back(cmd);
}
std::vector<Categories> categories = {
{"Easy workflows for plain text input/output", COMMAND_EASY},
{"Main workflows for dat... |
581cc1c514c1b832e6353deaed55e9e6450501885b79dc189e378e2adecfc135 | C++ | 5,617 | 162 | #include <cfloat>
#include <vector>
#include "caffe/layers/eltwise_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void EltwiseLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
const vector<Blob<Dtype>*>& top) {
CHECK(this->layer_param().eltwise_para... |
787f8de4d41ca04ec7a095f2bab3ed696e617fff4e413d421cb3536b9623f722 | C++ | 5,622 | 159 | /*********************************************************************
* __ _ _ _ _____
* / _| | | /\ | | | |/ ____|
* | |_ __ _ ___| |_ / \ | | | | |
* | _/ _` / __| __| / /\ \| | | | |
* | || (_| \__ \ |_ / ____ \ |__| | |____
* |_| \__,_|___... |
f6f82b413fc7715db0cd7b8a02ed5e54ccadd0557869aff8661003dccea3ff8f | C++ | 5,626 | 207 | /**
* Copyright 2017-2024 by XGBoost contributors
*/
#ifndef XGBOOST_USE_CUDA
#ifndef XGBOOST_USE_SYCL
// dummy implementation of HostDeviceVector in case CUDA is not used
#include <xgboost/base.h>
#include <xgboost/data.h>
#include <cstdint>
#include <memory>
#include <utility>
#include "xgboost/tree_model.h"
#inc... |
9e76804a8f433be619746e2152a751d8f1c6c35e097050679916f3fe10c25438 | C++ | 5,679 | 170 | /**
* Copyright 2019-2025, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/data.h>
#include <type_traits>
#include <utility>
#include "../../../src/data/adapter.h"
#include "../../../src/data/simple_dmatrix.h"
#include "../helpers.h"
#include "xgboost/base.h"
#include "xgboost/c_api.h"
namespac... |
d62c4d4b1b70dd3395eeec0aa3aefd01e0a2ee73d15a2a2032a005861fcff37a | C++ | 5,681 | 148 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "Orf.h"
#include <unordered_map>
#include <unordered_set>
#ifdef OPENMP
#include <omp.h>
#endif
int recoverlongestorf(int argc, const char **argv, const Command &command) {
Parameters &par = Paramete... |
c0d3a9b7175d066b6c953ca18410d0438695cb2bf83ec38c5276fee0002add6e | C++ | 5,711 | 87 | // Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include <Rcpp.h>
using namespace Rcpp;
#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(... |
ec84bb8e275a55bd6151db48918bb64911b0e6220af3733020f4b95177f44d0c | C++ | 5,734 | 141 | /**
* Copyright 2022-2024, XGBoost contributors
*/
#include "federated_tracker.h"
#include <grpcpp/security/server_credentials.h> // for InsecureServerCredentials, ...
#include <grpcpp/server_builder.h> // for ServerBuilder
#include <cstdint> // for int32_t
#include <exception> // for exception
#... |
a77418d287c6c5f1319d1ae085f9bc37fbafbe0630179217dd69b5cedfd54238 | C++ | 5,753 | 195 | /**
* Copyright 2018-2023, XGBoost Contributors
*/
#include "../../../src/common/random.h"
#include "../helpers.h"
#include "gtest/gtest.h"
#include "xgboost/context.h" // for Context
namespace xgboost::common {
namespace {
void TestBasic(Context const* ctx) {
int n = 128;
ColumnSampler cs{1u};
std::vector<fl... |
04afd094ccd3e82c8384b44e5fb4d540a5c042c56dbfac275323bdd646900e9d | C++ | 5,768 | 211 | /*++
Module Name:
CommandProcessor.cpp
Abstract:
Code for running the top-level commands of SNAP
Authors:
Bill Bolosky, November, 2014
Environment:
User mode service.
Revision History:
Pulled from the main program and expanded to handle daemon mode
--*/
#include "stdafx.h"
#include "options.... |
13fe1b934ed9c987703ee67d86362a54441a2169614e52c302f839a683241a49 | C++ | 5,796 | 203 | /*
* Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
#include "kraken2_headers.h"
#include "kv_store.h"
#include "mmscanner.h"
#include "seqreader.h"
#include "utilities.h"
#include <ios>
#include <stdio.h>
#include <unistd.h>
... |
0f7cb8764770db2c74e77daaeebe6b596b64a2c2009cac1a66a168718198ba88 | C++ | 5,823 | 350 | /******************************************************************
* *
* Copyright by Joachim Saul <saul@gfz-potsdam.de> *
* *
***********************************************... |
d7706b0bf37b89264ee5a610cdef7f28627baadfbb384c00a2001f09920a6fc5 | C++ | 5,829 | 152 | /**
* Copyright 2014-2024, XGBoost Contributors
* \file updater_refresh.cc
* \brief refresh the statistics and leaf value on the tree on the dataset
* \author Tianqi Chen
*/
#include <xgboost/tree_updater.h>
#include <limits>
#include <vector>
#include "../collective/allreduce.h"
#include "../common/threading_ut... |
06904f05d007d94a2f2d34a7fc661351071f53a7952f2f86fa84ff7548d8ce71 | C++ | 5,883 | 163 | #include "Parameters.h"
#include "DBWriter.h"
#include "Util.h"
#include "FileUtil.h"
#include "Debug.h"
#include "UniprotKB.h"
#include "GzReader.h"
#include <fstream>
#include <set>
#include <sstream>
std::string getPrimaryAccession(const std::string &accession) {
size_t end = accession.find_first_of(';');
... |
276708eafe4ceef3c3ca8f3795fc56a19fc60dcd1bcae901eba5718728182d91 | C++ | 5,902 | 150 | /**
* Copyright 2023 by XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/base.h> // for Args, bst_target_t
#include <xgboost/data.h> // for DMatrix, MetaInfo
#include <xgboost/json.h> // for Json, get, Object, String
#include <x... |
baf57823d1b92ee192e5652a1387fa637a834b8f1643c8f91eb994b468e90819 | C++ | 5,904 | 128 | #include "Util.h"
#include "Parameters.h"
#include "Matcher.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "NucleotideMatrix.h"
#include "SubstitutionMatrix.h"
#include "Alignment.h"
#include "itoa.h"
#ifdef OPENMP
#include <omp.h>
#endif
int parseproteomealignments(int argc, const char **... |
7747f0fd4b6dd16171bd89e64932441e1362ad4b145ce62125dfddab64080341 | C++ | 5,905 | 170 | /**
* Copyright 2023 by XGBoost contributors
*/
#include "ranking_utils.h"
#include <algorithm> // for copy_n, max, min, none_of, all_of
#include <cstddef> // for size_t
#include <cstdio> // for sscanf
#include <functional> // for greater
#include <string> // for c... |
65cf24c8d9ceb898dc69aea2b3a67dd12dbd92dddbab71a446a57ada2d1bbef4 | C++ | 6,003 | 246 | #include "stdafx.h" // pre-compiled headers
#include "defines.h"
#include "globaldata.h"
#include "script.h"
#include "application.h"
#include "script_object.h"
#include "script_func_impl.h"
#include "input_object.h"
ObjectMemberMd InputObject::sMembers[] =
{
#define BOOL_OPTION(OPT) md_property(InputObject, OPT, ... |
c7949d683590300d256e6758fb9351fa7e1cd44121796e5007ab730930be646b | C++ | 6,009 | 155 | #ifdef _OPENMP
#include <omp.h>
#endif
#include <Rcpp.h>
#include <string>
#include <vector>
#include "biconnected_component.h"
#include "confidence_cut.h"
#include "cycle_tracker.h"
#include "environment.h"
#include "orientation.h"
#include "r_cpp_interface.h"
#include "skeleton.h"
#include "utilities.h"
#include "t... |
21ceae82489ba21738ffe563f7decc18253998419b9301fd87844e1bfc109124 | C++ | 6,047 | 223 | /*++
Module Name:
BufferedAsync.cpp
Abstract:
Double-buffered asynchronous file I/O
Environment:
User mode service.
This class is NOT thread safe. It's the caller's responsibility to ensure that
at most one thread uses an instance at any time.
--*/
#include "stdafx.h"
#include "Compat.h"
#... |
bce472a4c727e125ae7b7e7fdc82e64f8baec3804055f4ce266118cb9a996ceb | C++ | 6,069 | 193 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
86735b310454ad11b4ce2e646622c4e4041f5c81b0b54e8df58ad51630de9e24 | C++ | 6,082 | 272 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
4f7a579578a131db9d1d2039b1bcfac55c73980554410462f62babc09255b02c | C++ | 6,083 | 282 | /*
* Copyright (c) 2016-present, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under both the BSD-style license (found in the
* LICENSE file in the root directory of this source tree) and the GPLv2 (found
* in the COPYING file in the root directory of this source tree).
*/
#include "util... |
66785da5e763be1dd937f2154d47dd140d3f5c6a3ea28263185526339d9cb56c | C++ | 6,134 | 154 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include <algorithm>
int appenddbtoindex(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true, Parameters::PARSE... |
1606e6af40c1d06fdd667f1a38f2a2adf26b003d045d303543fe1ff8e3e102b6 | C++ | 6,143 | 181 | // Copyright 2006, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
13468943b716f135151bd64b73c39dd42791d0ab40d8e82b3d88a644ad62ae5b | C++ | 6,172 | 188 | #ifdef USE_HDF5
/*
TODO:
- load file in a separate thread ("prefetch")
- can be smarter about the memcpy call instead of doing it row-by-row
:: use util functions caffe_copy, and Blob->offset()
:: don't forget to update hdf5_daa_layer.cu accordingly
- add ability to shuffle filenames if flag is set
*/
#include <fst... |
d88823244fec1e73225803a99f9318ea6c632255248193f224ae43103a970027 | C++ | 6,233 | 190 | // ReplaceDots2Ovals.c
//
// img=ReplaceDots2Ovals(img,dot_pos_idx,noise_dot_num,wdot,bdot,dotalpha,bgcolor,LR_flag)
//
// MEX function used in "sla_RDSfastest_with_noise_MEX" function
//
// Generate left/right Random Dot Stereogram (RDS) Image with gaussian
// filtered white/black dots
//
// [NOTE]
// This... |
51b9ed92e0a4bdf834e076e4c934287deda05b96f12ad944da02c73c47f8fa3c | C++ | 6,296 | 206 | /**
* Copyright 2020-2024 by XGBoost contributors
*/
#include <gtest/gtest.h>
#include <string>
#include <utility>
#include <vector>
#include "../../../plugin/sycl/common/partition_builder.h"
#include "../../../plugin/sycl/device_manager.h"
#include "../helpers.h"
namespace xgboost::sycl::common {
void TestPartit... |
43d9dbeffde1a5b837b88d86787c8732b30a8d1ed34c9dfb504cd54063622986 | C++ | 6,333 | 160 | #include "Debug.h"
#include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Matcher.h"
#include "Util.h"
#include "itoa.h"
#include "TranslateNucl.h"
#include "Orf.h"
#include <unistd.h>
#include <climits>
#include <algorithm>
#ifdef OPENMP
#include <omp.h>
#endif
int extractorfs(int argc, const... |
c3a26a7c9cc43af27e3b6775c24325900e65058b0680937cededb5e320675791 | C++ | 6,373 | 149 | /**
* Copyright 2018-2023 by XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/base.h> // for bst_bin_t
#include <xgboost/context.h> // for Context
#include <xgboost/data.h> // for BatchIterator, BatchSet, DMatrix, Met...
#include <cstddef> // for size_t
#include <cstdint> // for ... |
c06322db8e3c759130259d73314a0643d84c99a32956e4c6a0e655301485fa17 | C++ | 6,394 | 135 | // dear imgui: standalone example application for Allegro 5
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
#include <stdint.h>
#include <allegro5/allegro.h>
#include <allegro5/allegro_primitives.h>
#include "imgui.h"
#include "imgui_impl_allegro5.h"
int main(int, c... |
5816fb773a525c7a488ce4039241270715c6654d03a9e2ccfaf187b2cb80bc3c | C++ | 6,399 | 165 | #include <string>
#include <cstring>
#include <vector>
#include <sstream>
#include <algorithm>
#include "UniprotKB.h"
#include "Debug.h"
#include "Util.h"
const std::string UniprotKB::columnNames[] = {
"ID", "AC",
"DT", "DE", "GN",
"OS", "OG", "OC",
"OX", "OH", "REF",
"CC", "DR... |
c1c3cb279537be7c6395e261ea0bfbe0c8cef37deef2c8e0f59eb365eaf5bb3a | C++ | 6,412 | 176 | /*!
* Copyright 2017-2024 by Contributors
* \file gradient_index.cc
*/
#include <vector>
#include <limits>
#include <algorithm>
#include "gradient_index.h"
#include <sycl/sycl.hpp>
namespace xgboost {
namespace sycl {
namespace common {
uint32_t SearchBin(const bst_float* cut_values, const uint32_t* cut_ptrs, En... |
c54c0ea7120d29ae04d1d7c226ef5ed74cb18d3ab095c3377e2e1a16ec62e2bf | C++ | 6,506 | 200 | /**
* Copyright 2022-2024, XGBoost Contributors
*/
#include "xgboost/collective/socket.h"
#include <algorithm> // for max
#include <array> // for array
#include <cstddef> // for size_t
#include <cstdint> // for int32_t
#include <cstring> // for memcpy, memset
#include <system_error> //... |
7309b11f7a54b43ae193f3ca8e0dc0f8c0699b7d7f446c9ead21771988382499 | C++ | 6,526 | 165 | /**
* Copyright 2024-2025, XGBoost Contributors
*/
#include "extmem_quantile_dmatrix.h"
#include <memory> // for shared_ptr
#include <string> // for string
#include <vector> // for vector
#include "../common/error_msg.h" // for CacheHostRatio, InconsistentMaxBin
#include "../tree/param.h" // FIXME(ji... |
63d83339dc70dc98b8dd54625b3360fdc36270472c9a02c02a36a3b81be211b9 | C++ | 6,533 | 154 | // Computes MSAs from clustering or alignment result
#include <string>
#include <vector>
#include <sstream>
#include <Matcher.h>
#include <Orf.h>
#include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#ifdef OPENMP
#include <omp.h>
#endif
int result2dnamsa(int argc,... |
aee086339e93055cf6979f9ec5e0be96c7532f453a8409dabf9f9162c5dbbccd | C++ | 6,549 | 250 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
8caad8d1c97ff8336121f5ef2c1e5f7b6b75a3561fdc1019b4f6f873285e20c2 | C++ | 6,554 | 146 | // dear imgui: standalone example application for GLUT/FreeGLUT + OpenGL2, using legacy fixed pipeline
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
// !!! GLUT/FreeGLUT IS OBSOLETE SOFTWARE. Using GLUT is not recommended unless you really miss the 90's. !!!
// !!!... |
1a35bdeaebb0fae91e474d24bad8be01e1dca3d09207eada2a1b6459b84478ac | C++ | 6,555 | 170 | /**
* Copyright 2022-2025, XGBoost Contributors
*/
#include "adaptive.h"
#include <algorithm> // std::transform,std::find_if,std::copy,std::unique
#include <cmath> // std::isnan
#include <cstddef> // std::size_t
#include <iterator> // std::distance
#include <vector> // std::vector
#include "../common... |
21323f477a5e9d208c493897b800de23383b3ef10688184253c57e39fe83da8f | C++ | 6,586 | 224 | /*++
Module Name:
ToFASTQ.cpp
Abstract:
Take a set of reads in SAM or BAM format and convert them to FASTQ
Authors:
Bill Bolosky, January, 2014
Environment:
`
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "SAM.h"
#include "Bam.h"
#include "Genome.h"
#include "Compa... |
343a8960ba38d35cd3d476322d637fe29ffcfa7d6ab7418b2acb5594c52edb96 | C++ | 6,590 | 199 | // Copyright 2005, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
9656e22a960c3f10320c76dd1e7f12cfe363db467d449a984937e0df09a675be | C++ | 6,591 | 238 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
*
* eml_setop.cpp
*
* Code generation for function 'eml_setop'
*
*/
/* Include files */
#include "eml_setop.h"... |
04409cf0d69df6686e314f21199b8691b7e80dcd5adbd3f3b314867505b126c1 | C++ | 6,606 | 192 | // Copyright 2007, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
4c0a8cbaec18d7903c328023b3bf00ba5fdf3b4f2b87345d294eb6a046a233d4 | C++ | 6,667 | 171 | /*!
* Copyright 2019 by Contributors
*/
#include <gtest/gtest.h>
#include <fstream>
#include <string>
#include "../../../src/common/config.h"
#include "../filesystem.h" // dmlc::TemporaryDirectory
#include "../helpers.h"
namespace xgboost {
namespace common {
TEST(ConfigParser, NormalizeConfigEOL) {
// Test wh... |
cb86a6279c070578ce1e1ed83e4ce5be1af44c1593c171671a927190a4815435 | C++ | 6,676 | 261 | /*++
Module Name:
wc.cpp
Abstract:
Version of the standard wc (word count) program that uses 64 bit counters.
Authors:
Bill Bolosky, September, 2013
Revision History:
--*/
#include "stdafx.h"
#include "Compat.h"
#include "exit.h"
void usage()
{
fprintf(stderr,"usage: wc [-lwc] [files]\n");... |
2196568ae9864e65943bfff1672e4deac502e44e80fe107840bdbc9004e31031 | C++ | 6,686 | 196 | #include <cstdlib>
#include <fstream>
#include <sstream>
#include <algorithm>
#include <utility>
#include <climits>
#include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "FastSort.h"
#ifdef OPENMP
#include <omp.h>
#endif
struct compareSecondEntry {
bool
operator()(co... |
098c9e68cdb84ae7acb13a65884c0950357f34aeb843da99d3dbab4038e444de | C++ | 6,690 | 164 | #include "Debug.h"
#include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Matcher.h"
#include "Util.h"
#include "itoa.h"
#include "Orf.h"
#include <unistd.h>
#include <climits>
#include <algorithm>
#ifdef OPENMP
#include <omp.h>
#endif
int splitsequence(int argc, const char **argv, const Comm... |
3c0f57cf11cf266a1934c2471d06fbc2f0b5190733388d4164f64684e14d723f | C++ | 6,694 | 152 | #include "DBReader.h"
#include "CommandCaller.h"
#include "Util.h"
#include "FileUtil.h"
#include "Debug.h"
#include "PrefilteringIndexReader.h"
#include "LinsearchIndexReader.h"
#include "linsearch.sh.h"
namespace Linsearch {
#include "translated_search.sh.h"
}
#include <climits>
#include <cassert>
void setLinsear... |
ab5c869bf2a65cac29db7ae994b224475419fd0844859f929956b86c6a07f3e8 | C++ | 6,699 | 300 | #include <assert.h>
#include <iterator>
#include <sstream>
#include "yaml-cpp/exceptions.h"
#include "yaml-cpp/node/detail/memory.h"
#include "yaml-cpp/node/detail/node.h" // IWYU pragma: keep
#include "yaml-cpp/node/detail/node_data.h"
#include "yaml-cpp/node/detail/node_iterator.h"
#include "yaml-cpp/node/ptr.h"
#i... |
088f6fe74aa2423a74995c98e0f19d0ad47a0170831ea9b3e0674d4a746bb0ef | C++ | 6,702 | 174 | // Copyright 2007, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
aa98bcefa5ac13a083ac6e6a7e6dc51ef64dd70415365d131425cb9d521bc13d | C++ | 6,709 | 198 | // ReplaceDots2Ovals_with_noise.cpp
//
// img=ReplaceDots2Ovals_with_noise(img,noise_img,dot_pos_idx,noise_dot_num,wdot,bdot,dotalpha,bgcolor,LR_flag)
//
// MEX function used in "RDSfastest_with_noise_MEX" function
//
// Generate left/right Random Dot Stereogram (RDS) Image with gaussian
// filtered white/blac... |
7f4d36e32c4af4621a509fd7af8fee9c29c8759e24b1c25337f6c6ff276fa4ad | C++ | 6,731 | 204 | /**
* Copyright 2019-2024, XGBoost Contributors
*/
#include "gbtree_model.h"
#include <algorithm> // for transform, max_element
#include <cstddef> // for size_t
#include <numeric> // for partial_sum
#include <ostream> // for operator<<... |
2ba78f9123e7f8d0f0d589cba4ccabc6c29e920e336fdc554bfd2ed29e9e66ec | C++ | 6,775 | 171 | #include "Debug.h"
#include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Matcher.h"
#include "Util.h"
#include "TranslateNucl.h"
#include "Orf.h"
#include <unistd.h>
#include <climits>
#include <algorithm>
#ifdef OPENMP
#include <omp.h>
#endif
void handleSingleFrame(TranslateNucl& translateNu... |
4c4a2060c67fd982d2f21c30454224e7639ce004a917fabdc74971c0ecf4ae2d | C++ | 6,776 | 169 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "SubstitutionMatrix.h"
#include "tantan.h"
#include "Masker.h"
#ifdef OPENMP
#include <omp.h>
#endif
int makepaddedseqdb(int argc, const char **argv, const Command &command) {
Parameters &par = Parame... |
c8fde6f94f8f84e37381da1a0efad8f90bff8791d6dae2b79f049db7c3a41276 | C++ | 6,800 | 188 | /**
* Copyright 2024-2025, XGBoost Contributors
*/
#include "quantile_dmatrix.h"
#include <numeric> // for accumulate
#include "../collective/allreduce.h" // for Allreduce
#include "../collective/communicator-inl.h" // for IsDistributed
#include "../common/error_msg.h" // for InconsistentCateg... |
e43003013a08680d9619c0733be05b96322375f2e362af031c6bb8ce63b83140 | C++ | 6,917 | 348 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
f5e7f8fca119bda4f91bffe5eb3d4f41726b8021307e89c93e7a4a71734badbc | C++ | 6,935 | 147 | #include "Util.h"
#include "Parameters.h"
#include "Matcher.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "NucleotideMatrix.h"
#include "SubstitutionMatrix.h"
#include "Alignment.h"
#include "itoa.h"
#ifdef OPENMP
#include <omp.h>
#endif
int alignall(int argc, const char **argv, const Com... |
5ee42bd18e2689f10fdbb135dc8d3887beba53d4c2dfcba703ff38f6ba3df329 | C++ | 6,941 | 173 | // Copyright 2008 Google Inc.
// All Rights Reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions a... |
08f4537245a38ac8b0c76e96958145cb59017bdc21286492b66165505089034b | C++ | 6,946 | 179 | #ifdef USE_OPENCV
#include <opencv2/core/core.hpp>
#include <fstream> // NOLINT(readability/streams)
#include <iostream> // NOLINT(readability/streams)
#include <string>
#include <utility>
#include <vector>
#include "caffe/data_transformer.hpp"
#include "caffe/layers/base_data_layer.hpp"
#include "caffe/layers/imag... |
31ca2ea7b77716601bd2d0379da9be4f94f6dcb4ea65b3e9ac1dfc0d61ea961f | C++ | 6,965 | 212 | /**
* Copyright 2017-2024, XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/predictor.h>
#include "../../../src/collective/communicator-inl.h"
#include "../../../src/data/adapter.h"
#include "../../../src/data/proxy_dmatrix.h"
#include "../../../src/gbm/gbtree.h"
#include "../../../src/gbm/gbtree_m... |
29997e2104c784b3dbae9254b12a29c5f912996f674a9bb183141beb17a859fb | C++ | 6,984 | 183 | // Copyright 2008, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
3b247bfc94f24ccd966b17404ea32a3153fac7f068265101fc5ffbca1f0fa473 | C++ | 6,984 | 250 | #include "scanscalar.h"
#include <algorithm>
#include "exp.h"
#include "regeximpl.h"
#include "stream.h"
#include "yaml-cpp/exceptions.h" // IWYU pragma: keep
namespace YAML {
// ScanScalar
// . This is where the scalar magic happens.
//
// . We do the scanning in three phases:
// 1. Scan until newline
// 2. Ea... |
c2be6cb92c3f6b5c62924300d02b84682d3d6226085780ac476d6842638601c1 | C++ | 7,060 | 211 | #ifdef USE_HDF5
#include "caffe/util/hdf5.hpp"
#include <string>
#include <vector>
namespace caffe {
// Verifies format of data stored in HDF5 file and reshapes blob accordingly.
template <typename Dtype>
void hdf5_load_nd_dataset_helper(
hid_t file_id, const char* dataset_name_, int min_dim, int max_dim,
Bl... |
60fc512dd10e61ca178b12e8150d934739b8c9c29d041aad488a428785a606be | C++ | 7,069 | 266 |
///////////////////////////////////////////////////////////////////////////////
//
// AutoIt
//
// Copyright (C)1999-2003:
// - Jonathan Bennett <jon@hiddensoft.com>
// - Others listed at http://www.autoitscript.com/autoit3/docs/credits.htm
//
// This program is free software; you can redistribute it and/or modify
/... |
b54e86c46c7c3283653dd2cb7f5e440ea3f6a3822de01746dd5f0937886e4cc9 | C++ | 7,070 | 231 | #include <climits>
#include "BaseMatrix.h"
#include "simd.h"
#include "Debug.h"
#include "Util.h"
#include "MathUtil.h"
#include "Sequence.h"
const double BaseMatrix::ANY_BACK = 1E-5;
BaseMatrix::BaseMatrix(){
// init [amino acid <-> int] mappings
num2aa = new char[255];
aa2num = new unsigned char[stati... |
746568b938d9a9b6ed890cb1e0260b98a192f3578e3097f412df19d9ae070243 | C++ | 7,099 | 171 | /*
This file is part of the Firmware project to interface with small Async or Neuromorphic chips
Copyright (C) 2023 Ole Richter - University of Groningen
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fre... |
a816b881840c19e821b2b12aacc163f7ad3859bb8f1d9bc01b40a564689c637a | C++ | 7,114 | 169 | #include <cassert>
#include "LinsearchIndexReader.h"
#include "PrefilteringIndexReader.h"
#include "FileUtil.h"
#include "CommandCaller.h"
#include "Util.h"
#include "Debug.h"
#include "Parameters.h"
#include "easysearch.sh.h"
void setEasySearchDefaults(Parameters *p, bool linsearch) {
if (linsearch) {
p->... |
7545fc3b570a6b9f3618015d0f6d109eab4151040b5b0d7a3923b194446df21f | C++ | 7,125 | 209 | /**
* Copyright 2023-2024, XGBoost Contributors
*/
#include <gtest/gtest.h> // for ASSERT_EQ
#include <xgboost/span.h> // for Span, oper...
#include <algorithm> // for min
#include <chrono> // for seconds
#include <cstddef> // for size_t
#include <cstdint> // for int32_t
#include <numeric> // for io... |
62ecfaa0049a1b1b13aacd69958a924f6dfd6ea83f0f027da594c82e499e9ccf | C++ | 7,151 | 193 | #include "SubstitutionMatrix.h"
#include "Parameters.h"
#include "Sequence.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "MathUtil.h"
#include "FileUtil.h"
#ifdef OPENMP
#include "omp.h"
#endif
void parseHMM(char *data, std::string *sequence, std::string *header, char *p... |
55a93c9566921c9179b5f3350eb551d0f252f04408b5c0425c1c179f14a3e6b5 | C++ | 7,170 | 233 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* ... |
4c9583566f0536ce716ea6fc747d5ea08eee7ee23838dad3e847bb2211329c3b | C++ | 7,189 | 237 | /**
* Copyright 2019-2025, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <cstddef> // for size_t
#include <fstream> // for ofstream
#include <numeric> // for iota
#include "../../../src/common/io.h"
#include "../filesystem.h" // dmlc::TemporaryDirectory
#include "../helpers.h"
namespace xgboost::co... |
78c27ce39f6a4d09db6394609d0976fd0c6be48ffdbe2d5dd6c12c3c1f44480a | C++ | 7,208 | 156 | #include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "FastSort.h"
#include "Parameters.h"
#ifdef OPENMP
#include <omp.h>
#endif
int createclusearchdb(int argc, const char **argv, const Command& command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(arg... |
8ca369bce6910f40472d2549a363eaa65cde499357d6854c5b09281910764809 | C++ | 7,231 | 287 | #include "MuscleLimitConstraint.h"
#include "dart/external/odelcpsolver/lcp.h"
#include "Muscle.h"
#define DART_ERROR_ALLOWANCE 0.0
#define DART_ERP 0.01
#define DART_MAX_ERV 1e+1
#define DART_CFM 1e-9
double MuscleLimitConstraint::mErrorAllowance = DART_ERROR_ALLOWANCE;
double MuscleLimitConstraint::mErrorReductionP... |
cffae7fa372e6b1f55f09bdc3dbebb72d79e0104f1805f2126957bddbab4b35d | C++ | 7,299 | 315 | /*
* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of ... |
e19d9b2e29b5d93bfff373ef972d55334e457001b1d1a263021adc76e3da0eda | C++ | 7,335 | 224 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
8672cb971fadcdd9b46c48b6e105cafaf58945ab540085b652e57046a0128e64 | C++ | 7,342 | 263 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
ef740ac34f93d20175b637773d1c664d60c8d436249b3a88f8ac3eae63868d08 | C++ | 7,343 | 224 | /**
* Copyright 2024-2025, XGBoost contributors
*/
#if defined(XGBOOST_USE_CUDA)
#include "cuda_dr_utils.h"
#include <algorithm> // for max
#include <cstdint> // for int32_t
#include <cstring> // for memset
#include <memory> // for make_unique
#include <mutex> // for call_once
#include <sstream> /... |
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